FIXED.
I thought about the Windows Registry. Ran regedit and looked around. Found the key HKEY_CURRENT_USER > Software > Tequila > Settings.
Had a "params" string that was empty, "". Hmmm, if Tequila chose to use the Registery params over the Tequila.xml params, then Tequila would run SCORE without -noversioncheck.....
Deleted the whole HKEY_CURRENT_USER > Software > Tequila key, then reran Tequila.
Tequila asked for the directory to install City in, told it to use the one it was already in, and off it went. Updated a few .pigg's and started the City client. Logged in.
And could go on all 4 Shards!!!
I checked afterwards with regedit. That value HKEY_CURRENT_USER > Software > Tequila > params has not been recreated. And now I know to check there.
And now I'm very happy I've fixed this issue.